The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known...The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methyl- ations and pseudouridylation are required for normal develop- ment in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6-methyladenosine （m^6A）, 5-methylcytosine （m^5C）, pseudour- idine （up）, and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.展开更多
Tomato(Solanum lycopersicum)is an extensively cultivated vegetable,and its growth and fruit quality can be significantly impaired by low temperatures.The widespread presence of N^(6)-methyladenosine(m^(6)A)modificatio...Tomato(Solanum lycopersicum)is an extensively cultivated vegetable,and its growth and fruit quality can be significantly impaired by low temperatures.The widespread presence of N^(6)-methyladenosine(m^(6)A)modification on RNA is involved in a diverse range of stress response processes.There is a significant knowledge gap regarding the precise roles of m^(6)A modification in tomato,particularly for cold stress response.Here,we assessed the m^(6)A modification landscape of S.lycopersicum'Micro-Tom'leaves in response to low-temperature stress.Furthermore,we investigated the potential relationship among m^(6)A modification,transcriptional regulation,alternative polyadenylation events,and protein translation via MeRIP-seq,RNA-seq,and protein mass spectrometry.After omic date analysis,11378 and 10735 significant m^(6)A peak associated genes were identified in the control and cold treatment tomato leaves,respectively.Additionally,we observed a UGUACAK(K=G/U)motif under both conditions.Differential m^(6)A site associated genes most likely play roles in protein translation regulatory pathway.Besides directly altering gene expression levels,m^(6)A also leads to differential poly(A)site usage under low-temperature.Finally,24 important candidate genes associated with cold stress were identified by system-level multi-omic analysis.Among them,m^(6)A modification levels were increased in SBPase(Sedoheptulose-1,7-bisphosphatase,Solyc05g052600.4)mRNA,causing distal poly(A)site usage,downregulation of mRNA expression level,and increased protein abundance.Through these,tomato leaves try to maintain normal photo synthetic carbon assimilation and nitro gen metabolism under low-temperature condition.The comprehensive investigation of the m^(6)A modification landscape and multi-omics analysis provide valuable insights into the epigenetic regulatory mechanisms in tomato cold stress response.展开更多
N6-methyladenosine(m^(6)A)modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function.The m^(6)A reader YTHDF1 has been shown to enhance the transl...N6-methyladenosine(m^(6)A)modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function.The m^(6)A reader YTHDF1 has been shown to enhance the translational efficiency of m^(6)A-modified mRNAs in the brain and is essential for learning and memory.However,its role in the mature retina remains unclear.Herein,we report a novel role of Ythdf1 in the maintenance of retinal function using a genetic knockout model.Loss of Ythdf1 resulted in impaired scotopic electroretinogram(ERG)responses and progressive retinal degeneration.Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects.Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in Ythdf1-deficient retinas.Integrative analysis of methylated RNA immunoprecipitation(MeRIP)sequencing and RIP sequencing identified Tulp1 and Dhx38,two inheritable retinal degeneration disease-associated gene homologs,as direct targets of YTHDF1 in the retina.Specifically,YTHDF1 recognized and bound m^(6)A-modified Tulp1 and Dhx38 mRNA at the coding sequence(CDS),enhancing their translational efficiency without altering mRNA levels.Collectively,these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m^(6)A reader proteins in retinal degeneration,identifying potential therapeutic targets for severe retinopathies.展开更多
The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying mechanisms.Methylation of N6 adenosine(m^(6)A)and C5 cytosine(m^(5)C)bases occur on mRNA...The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying mechanisms.Methylation of N6 adenosine(m^(6)A)and C5 cytosine(m^(5)C)bases occur on mRNAs,tRNA,mt-tRNA,and rRNA species as well as non-coding RNAs.With emerging knowledge of RNA binding proteins that act as writer,reader,and eraser effector proteins,comes a new understanding of physiological processes controlled by these systems.Such processes when spatiotemporally disrupted within cellular nanodomains in highly specialized tissues such as the brain,give rise to different forms of disease.In this review,we discuss accumulating evidence that changes in the m^(6)A and m^(5)C methylation systems contribute to neurocognitive disorders.Early studies first identified mutations within FMR1 to cause intellectual disability Fragile X syndromes several years before FMR1 was identified as an m^(6)A RNA reader protein.Subsequently,familial mutations within the m^(6)A writer gene METTL5,m^(5)C writer genes NSUN2,NSUN3,NSUN5,and NSUN6,as well as THOC2 and THOC6 that form a protein complex with the m^(5)C reader protein ALYREF,were recognized to cause intellectual development disorders.Similarly,differences in expression of the m^(5)C writer and reader effector proteins,NSUN6,NSUN7,and ALYREF in brain tissue are indicated in individuals with Alzheimer's disease,individuals with a high neuropathological load or have suffered traumatic brain injury.Likewise,an abundance of m^(6)A reader and anti-reader proteins are reported to change across brain regions in Lewy bodies diseases,Alzheimer's disease,and individuals with high cognitive reserve.m^(6)A-modified RNAs are also reported significantly more abundant in dementia with Lewy bodies brain tissue but significantly reduced in Parkinson's disease tissue,whilst modified RNAs are misplaced within diseased cells,particularly where synapses are located.In parahippocampal brain tissue,m^(6)A modification is enriched in transcripts associated with psychiatric disorders including conditions with clear cognitive deficits.These findings indicate a diverse set of molecular mechanisms are influenced by RNA methylation systems that can cause neuronal and synaptic dysfunction underlying neurocognitive disorders.Targeting these RNA modification systems brings new prospects for neural regenerative therapies.展开更多
Inherited retinal dystrophies (IRDs) are major causes of visual impairment and irreversible blindness worldwide, while the precise molecular and genetic mechanisms are still elusive. N6-methyladenosine (m^(6)A) modifi...Inherited retinal dystrophies (IRDs) are major causes of visual impairment and irreversible blindness worldwide, while the precise molecular and genetic mechanisms are still elusive. N6-methyladenosine (m^(6)A) modification is the most prevalent internal modification in eukaryotic mRNA. YTH domain containing 2 (YTHDC2), an m^(6)A reader protein, has recently been identified as a key player in germline development and human cancer. However, its contribution to retinal function remains unknown. Here, we explore the role of YTHDC2 in the visual function of retinal rod photoreceptors by generating rod-specific Ythdc2 knockout mice. Results show that Ythdc2 deficiency in rods causes diminished scotopic ERG responses and progressive retinal degeneration. Multi-omics analysis further identifies Ppef2 and Pde6b as the potential targets of YTHDC2 in the retina. Specifically, via its YTH domain, YTHDC2 recognizes and binds m^(6)A-modified Ppef2 mRNA at the coding sequence and Pde6b mRNA at the 5′-UTR, resulting in enhanced translation efficiency without affecting mRNA levels. Compromised translation efficiency of Ppef2 and Pde6b after YTHDC2 depletion ultimately leads to decreased protein levels in the retina, impaired retinal function, and progressive rod death. Collectively, our finding highlights the importance of YTHDC2 in visual function and photoreceptor survival, which provides an unreported elucidation of IRD pathogenesis via epitranscriptomics.展开更多
BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic comp...BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic complication,usually occurs at an earlier age and progresses faster than age-related cataracts.Evidence has linked N6-methyladenosine(m6A)to DC progression.However,there exists a lack of understanding regarding RNA m6A modifications and the role of m6A in DC pathogenesis.AIM To elucidate the role played by altered m6A and differentially expressed mRNAs(DEmRNAs)in DC.METHODS Anterior lens capsules were collected from the control subjects and patients with DC.M6A epitranscriptomic microarray was performed to investigate the altered m6A modifications and determine the DEmRNAs.Through Gene Ontology and pathway enrichment(Kyoto Encyclopedia of Genes and Genomes)analyses,the potential role played by dysregulated m6A modification was predicted.Real-time polymerase chain reaction was further carried out to identify the dysregulated expression of RNA methyltransferases,demethylases,and readers.RESULTS Increased m6A abundance levels were found in the total mRNA of DC samples.Bioinformatics analysis predicted that ferroptosis pathways could be associated with m6A-modified mRNAs.The levels of five methylation-related genes-RBM15,WTAP,ALKBH5,FTO,and YTHDF1-were upregulated in DC samples.Upregulation of RBM15 expression was verified in SRA01/04 cells with high-glucose medium and in samples from DC patients.CONCLUSION M6a mRNA modifications may be involved in DC progression via the ferroptosis pathway,rendering novel insights into therapeutic strategies for DC.展开更多
N6-methyladenosine(m^(6)A)modification,the most abundant internal modification in messenger RNA(mRNA)and long non-coding RNA(lncRNA),has emerged as a critical epitranscriptomic regulatory mechanism in eukaryotes.While...N6-methyladenosine(m^(6)A)modification,the most abundant internal modification in messenger RNA(mRNA)and long non-coding RNA(lncRNA),has emerged as a critical epitranscriptomic regulatory mechanism in eukaryotes.While the importance of m^(6)A modification in various biological processes has been recognized,a comprehensive understanding of its diverse roles in plant biology and agricultural applications remains fragmented.This review analyzes recent advances inm^(6)A modification's biological functions in plants.m^(6)A modification plays crucial roles in multiple aspects of plant life,including seed germination,organ development,and reproductive structure formation.Furthermore,m^(6)A has been found to significantly influence plant responses to environmental stresses,including salt,drought,temperature,and heavy metal exposure.We also uncover m^(6)A involvement in important agricultural traits.This review provides insights into the mechanistic understanding of m^(6)A modification in plants and highlights its applications in agricultural improvement,offering a foundation for future research in crop enhancement and stress resistance.展开更多
Proper ovarian follicle development,which is required for the maintenance of female fertility,is critical for the production of mature oocytes[1,2].Meanwhile,the correct establishment of the epitranscriptome in oocyte...Proper ovarian follicle development,which is required for the maintenance of female fertility,is critical for the production of mature oocytes[1,2].Meanwhile,the correct establishment of the epitranscriptome in oocytes is essential for precise gene repression and the acquisition of developmental competence[1–5].The ac4C modification is the third most abundant chemical modification in transcriptome[6,7].NAT10,the only known writer of ac4C,has been shown to participate in physiological and disease settings[6,8–11].However,NAT10-targeted transcripts in oocytes as well as their functions in supporting folliculogenesis are poorly understood.展开更多
Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in the process of plant stress adaptation.Currently,over 170 distinct chemical modifications have been identified in mRNAs,...Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in the process of plant stress adaptation.Currently,over 170 distinct chemical modifications have been identified in mRNAs,tRNAs,rRNAs,microRNAs(miRNAs),and long noncoding RNAs(lncRNAs).Genetic and molec-ular studies have identified the genes responsible for addition and removal of chemical modifications from RNA molecules,which are known as"writers"and"erasers,"respectively.N^(6)-methyladenosine(m^(6)A)is the most prevalent chemical modification identified in eukaryotic mRNAs.Recent studies have identified m6 A writers and erasers across different plant species,including Arabidopsis(Arabidopsis thaliana),rice(Oryza sativa),cotton(Gossypium hirsutum),and tomato(Solanum lycopersicum).Accumulating discoveries have improved our understanding of the functions of RNA modifications in plant stress responses.This review highlights the latest research on RNA modification,emphasizing the biological and cellular roles of diverse chemical modifications of mRNAs,tRNAs,rRNAs,miRNAs,and lncRNAs in plant responses to environ-mental and hormonal signals.We also propose and discuss critical questions and future challenges for enhancing our understanding of the cellular and mechanistic roles of RNA modifications in plant stress re-sponses.Integrating molecular insights into the regulatory roles of RNA modifications in stress responses with novel genome-and RNA-editing technologies will facilitate the breeding of stress-tolerant crops through precise engineering of RNA modifications.展开更多
5-methylcytosine(m^(5)C)is a prevalent RNA modification that has various impacts on m RNA fate.Here,we generated 30 single-base resolution RNA m^(5)C methylomes and revealed the dynamic nature of m^(5)C of heart,muscl...5-methylcytosine(m^(5)C)is a prevalent RNA modification that has various impacts on m RNA fate.Here,we generated 30 single-base resolution RNA m^(5)C methylomes and revealed the dynamic nature of m^(5)C of heart,muscle,lung,esophagus,stomach,pancreas,colon,jejunum,and rectum from 7 adult human individuals using RNA-Bis Seq.Based on clustering analysis,the heart and muscle formed one cluster,while the remaining tissues constituted another cluster.Intriguingly,we observed a discrepancy pattern between m^(5)C levels and gene expression in these tissues when comparing the m^(5)C methylome and transcriptome.Moreover,we identified differences in NSUN2-mediated m^(5)C modifications between esophageal paracancerous tissues and healthy individual tissues.Notably,NSUN2 was found to interact with PLXNA1 m RNA,and silencing NSUN2 in esophageal squamous cell carcinoma(ESCC)cells resulted in the downregulation of PLXNA1 expression through an m^(5)C-mediated mechanism.Overall,our study provides valuable insights into the m^(5)C profile and the relationship between the methylome and transcriptome in human tissues,highlighting the potential role of m^(5)C modification as an epitranscriptomic biomarker.展开更多
Male fertility is built on the proper proliferation and differentiation of germline cells within the seminiferous epithelium in the testis,which continuously produces millions of sperm per day in mammals[1].RNA modifi...Male fertility is built on the proper proliferation and differentiation of germline cells within the seminiferous epithelium in the testis,which continuously produces millions of sperm per day in mammals[1].RNA modifications are emerging as crucial epitranscriptomic regulators.展开更多
The emerging field of epitranscriptomics has revolutionized our understanding of post-transcriptional regulation in plant systems.This review focuses on cutting-edge discoveries in the area of RNA modification,with a ...The emerging field of epitranscriptomics has revolutionized our understanding of post-transcriptional regulation in plant systems.This review focuses on cutting-edge discoveries in the area of RNA modification,with a particular emphasis on the N^(6)-methyladenosine(m^(6)A)-mediated regulatory networks that govern plant development and fruit maturation.We systematically summarize the spatiotemporal patterns of RNA modifications and their integration into phytohormone signaling cascades and responses to environmental stimuli.Advanced epitranscriptome sequencing platforms have identified evolutionarily conserved modification signatures across angiosperm species,while simultaneously revealing species-specific regulatory architectures.Despite substantial progress,our understanding of the molecular mechanisms that underlie RNA modifications,especially those other than m^(6)A,remains limited.We propose an innovative roadmap that combines CRISPR-based writer/eraser manipulation,single-cell spatial epitranscriptomics,and synthetic biology approaches to harness RNA modification networks for precision agriculture.We also underscore the importance of interdisciplinary collaboration that integrates findings from biology,chemistry,physics,and computer science to decode the plant epitranscriptome.To enable precise control of postharvest physiology,future priorities should include the development of biosensors for specific modification types,the engineering of RNA modification–dependent translation control systems,and the development of RNA epigenetic editing tools.展开更多
For a long time,mutations that do not alter protein sequences,so-called synonymous mutations,were largely overlooked.Scientists assumed they had little to no biological impact,considering them as neutral background no...For a long time,mutations that do not alter protein sequences,so-called synonymous mutations,were largely overlooked.Scientists assumed they had little to no biological impact,considering them as neutral background noise in the course of evolution.But a new study by Xin et al.(2025)challenges that assumption.Their research reveals that one such"silent"mutation played a pivotal role in cucumber domestication(Che and Zhang,2019).Rather than being inert,the mutation triggered a cascade of molecular changes involving mRNA structure and chemical modifications,ultimately altering hormone levels and growth patterns.These findings mark a turning point in our understanding of gene regulation,exposing RNA,not just DNA or protein,as a major driver of evolutionary change.展开更多
Colorectal cancer(CRC)continues to be the third most frequently diagnosed cancer,and the second leading cause of cancer-related mortality.Several non-invasive biomarkers have emerged,but only a few have been incorpora...Colorectal cancer(CRC)continues to be the third most frequently diagnosed cancer,and the second leading cause of cancer-related mortality.Several non-invasive biomarkers have emerged,but only a few have been incorporated into clinical practice due to the lack of sensitivity.1 Research on the epigenome has unveiled potential clinical applications for diagnosis and therapy response.2,3 Particularly,recent evidence suggests a novel role of RNA methylation in the development of CRC,4 revealing an overall RNA m6A hypomethylation.5 However,our understanding of their contribution to CRC remains limited.展开更多
Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many importan...Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N^6-methyladenosine （m^6A） is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs （lncRNAs）. In mammalian cells, m^6A can be incorporated by a methyltransferase complex and removed by demethy- lases, which ensures that the m^6A modification is reversible and dynamic. Moreover, m^6A is recognized by the YT521-B homology （YTH） domain-containing proteins, which subsequently direct different complexes to regulate RNA signaling pathways, such as RNA metabolism, RNA splicing, RNA folding, and protein translation. Herein, we summarize the recent progresses made in understanding the molecular mechanisms underlying the m^6A recognition by YTH domaincontaining proteins, which would shed new light on m^6A-specific recognition and provide clues to the future identification of reader proteins of many other RNA modifications.展开更多
More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from Na-methyladeno...More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from Na-methyladenosine （m6A）, N1-methyladenosine （mXA） has been found as a reversible modification in tRNA and mRNA. mlA occurs at positions 9, 14, and 58 of tRNA, with m1A58 being critical for tRNA stability. Other than the hundreds of m1A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1A also identifies 〉 20 m1A sites in mitochondrial genes, m1A in the coding region of mitochondrial transcripts can inhibit the translation of the corresponding proteins. In this review, we summarize the current understanding of mlA in mRNA and tRNA, covering high-throughput sequencing methods developed for m1A methylome, m1A-related enzymes （writers and erasers）, as well as its functions in mRNA and tRNA.展开更多
N6-Methyladenosine(m^(6)A)is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation,including transcriptional and post-transcriptional regulation.m^...N6-Methyladenosine(m^(6)A)is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation,including transcriptional and post-transcriptional regulation.m^(6)A is a reversible modification that is installed,removed,and recognized by methyltransferases(writers),demethylases(erasers),and m^(6)A-binding proteins(readers),respectively.Recently,the breadth of research on m^(6)A in plants has expanded,and the vital roles of m^(6)A in plant development,biotic and abiotic stress responses,and crop trait improvement have been investigated.In this review,we discuss recent developments in research on m^(6)A and highlight the detection methods,distribution,regulatory proteins,and molecular and biological functions of m^(6)A in plants.We also offer some perspectives on future investigations,providing direction for subsequent research on m^(6)A in plants.展开更多
2′-O-methylation(Nm)is one of the most abundant RNA epigenetic modifications and plays a vital role in the post-transcriptional regulation of gene expression.Current Nm mapping approaches are normally limited to high...2′-O-methylation(Nm)is one of the most abundant RNA epigenetic modifications and plays a vital role in the post-transcriptional regulation of gene expression.Current Nm mapping approaches are normally limited to highly abundant RNAs and have significant technical hurdles in m RNAs or relatively rare non-coding RNAs(nc RNAs).Here,we developed a new method for enriching Nm sites by using RNA exoribonuclease and periodate oxidation reactivity to eliminate 2′-hydroxylated(2′-OH)nucleosides,coupled with sequencing(Nm-REP-seq).We revealed several novel classes of Nm-containing nc RNAs as well as m RNAs in humans,mice,and drosophila.We found that some novel Nm sites are present at fixed positions in different t RNAs and are potential substrates of fibrillarin(FBL)methyltransferase mediated by sno RNAs.Importantly,we discovered,for the first time,that Nm located at the 3′-end of various types of nc RNAs and fragments derived from them.Our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.展开更多
Acetylation of N^(4)-cytidine(ac^(4)C)has recently been discovered as a novel modification of mRNA.RNA ac^(4)C modification has been shown to be a key regulator of RNA stability,RNA translation,and the thermal stress ...Acetylation of N^(4)-cytidine(ac^(4)C)has recently been discovered as a novel modification of mRNA.RNA ac^(4)C modification has been shown to be a key regulator of RNA stability,RNA translation,and the thermal stress response.However,its existence in eukaryotic mRNAs is still controversial.In plants,the existence,distribution pattern,and potential function of RNA ac^(4)C modification are largely unknown.Here we report the presence of ac^(4)C in the mRNAs of both Arabidopsis thaliana and rice(Oryza sativa).By comparing two ac^(4)C sequencing methods,we found that RNA immunoprecipitation and sequencing(acRIP-seq),but not ac^(4)C sequencing,was suitable for plant RNA ac^(4)C sequencing.We present transcriptome-wide atlases of RNA ac^(4)C modification in A.thaliana and rice mRNAs obtained by acRIP-seq.Analysis of the distribution of RNA ac^(4)C modifications showed that ac^(4)C is enriched near translation start sites in rice mRNAs and near translation start sites and translation end sites in Arabidopsis mRNAs.The RNA ac^(4)C modification level is positively correlated with RNA half-life and the number of splicing variants.Similar to that in mammals,the translation efficiency of ac^(4)C target genes is significantly higher than that of other genes.Our in vitro translation results confirmed that RNA ac^(4)C modification enhances translation efficiency.We also found that RNA ac^(4)C modification is negatively correlated with RNA structure.These results suggest that ac^(4)C is a conserved mRNA modification in plants that contributes to RNA stability,splicing,translation,and secondary structure formation.展开更多
The epitranscriptomic mark N6-methyladenosine(m^(6)A),which is the predominant internal modification in RNA,is important for plant responses to diverse stresses.Multiple environmental stresses caused by the tea-wither...The epitranscriptomic mark N6-methyladenosine(m^(6)A),which is the predominant internal modification in RNA,is important for plant responses to diverse stresses.Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor.However,the effects of the m^(6)A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized.We performed an integrated RNA methylome and transcriptome analysis to explore the m^(6)Amediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea(Camellia sinensis)leaves under solar-withering conditions.Dynamic changes in global m^(6)A level in tea leaves were mainly controlled by two m^(6)A erasers(CsALKBH4A and CsALKBH4B)during solar-withering treatments.Differentially methylated peak-associated genes following solarwithering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways.Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid,catechin,and theaflavin contents by triggering alternative splicing-mediated regulation.Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m^(6)A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.展开更多
基金supported by ARC grants DP110103805 and FT13100525 awarded to I.S.and an APA and a GRDC PhD topup scholarship awarded to A.B.
文摘The advent of high-throughput sequencing technol- ogies coupled with new detection methods of RNA modifica- tions has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over loo known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methyl- ations and pseudouridylation are required for normal develop- ment in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6-methyladenosine （m^6A）, 5-methylcytosine （m^5C）, pseudour- idine （up）, and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.
基金financially supported by the National Natural Science Foundation of China(Grant Nos.32202518 and 32070601)Shandong University of Technology PhD Start-up Fund(418097)。
文摘Tomato(Solanum lycopersicum)is an extensively cultivated vegetable,and its growth and fruit quality can be significantly impaired by low temperatures.The widespread presence of N^(6)-methyladenosine(m^(6)A)modification on RNA is involved in a diverse range of stress response processes.There is a significant knowledge gap regarding the precise roles of m^(6)A modification in tomato,particularly for cold stress response.Here,we assessed the m^(6)A modification landscape of S.lycopersicum'Micro-Tom'leaves in response to low-temperature stress.Furthermore,we investigated the potential relationship among m^(6)A modification,transcriptional regulation,alternative polyadenylation events,and protein translation via MeRIP-seq,RNA-seq,and protein mass spectrometry.After omic date analysis,11378 and 10735 significant m^(6)A peak associated genes were identified in the control and cold treatment tomato leaves,respectively.Additionally,we observed a UGUACAK(K=G/U)motif under both conditions.Differential m^(6)A site associated genes most likely play roles in protein translation regulatory pathway.Besides directly altering gene expression levels,m^(6)A also leads to differential poly(A)site usage under low-temperature.Finally,24 important candidate genes associated with cold stress were identified by system-level multi-omic analysis.Among them,m^(6)A modification levels were increased in SBPase(Sedoheptulose-1,7-bisphosphatase,Solyc05g052600.4)mRNA,causing distal poly(A)site usage,downregulation of mRNA expression level,and increased protein abundance.Through these,tomato leaves try to maintain normal photo synthetic carbon assimilation and nitro gen metabolism under low-temperature condition.The comprehensive investigation of the m^(6)A modification landscape and multi-omics analysis provide valuable insights into the epigenetic regulatory mechanisms in tomato cold stress response.
基金supported by the National Natural Science Foundation of China(82371083,82471100,82121003,82271084)Program of Science and Technology International Cooperation Project of Qinghai province(China)(2022-HZ-814)。
文摘N6-methyladenosine(m^(6)A)modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function.The m^(6)A reader YTHDF1 has been shown to enhance the translational efficiency of m^(6)A-modified mRNAs in the brain and is essential for learning and memory.However,its role in the mature retina remains unclear.Herein,we report a novel role of Ythdf1 in the maintenance of retinal function using a genetic knockout model.Loss of Ythdf1 resulted in impaired scotopic electroretinogram(ERG)responses and progressive retinal degeneration.Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects.Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in Ythdf1-deficient retinas.Integrative analysis of methylated RNA immunoprecipitation(MeRIP)sequencing and RIP sequencing identified Tulp1 and Dhx38,two inheritable retinal degeneration disease-associated gene homologs,as direct targets of YTHDF1 in the retina.Specifically,YTHDF1 recognized and bound m^(6)A-modified Tulp1 and Dhx38 mRNA at the coding sequence(CDS),enhancing their translational efficiency without altering mRNA levels.Collectively,these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m^(6)A reader proteins in retinal degeneration,identifying potential therapeutic targets for severe retinopathies.
基金funded by Notingham University and the Neuroscience Support Group Charity,UK(to HMK)supported by a CONACYT PhD scholarshipMD?was supported by the Postdoctoral Research Fellowship Program of TUBITAK。
文摘The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying mechanisms.Methylation of N6 adenosine(m^(6)A)and C5 cytosine(m^(5)C)bases occur on mRNAs,tRNA,mt-tRNA,and rRNA species as well as non-coding RNAs.With emerging knowledge of RNA binding proteins that act as writer,reader,and eraser effector proteins,comes a new understanding of physiological processes controlled by these systems.Such processes when spatiotemporally disrupted within cellular nanodomains in highly specialized tissues such as the brain,give rise to different forms of disease.In this review,we discuss accumulating evidence that changes in the m^(6)A and m^(5)C methylation systems contribute to neurocognitive disorders.Early studies first identified mutations within FMR1 to cause intellectual disability Fragile X syndromes several years before FMR1 was identified as an m^(6)A RNA reader protein.Subsequently,familial mutations within the m^(6)A writer gene METTL5,m^(5)C writer genes NSUN2,NSUN3,NSUN5,and NSUN6,as well as THOC2 and THOC6 that form a protein complex with the m^(5)C reader protein ALYREF,were recognized to cause intellectual development disorders.Similarly,differences in expression of the m^(5)C writer and reader effector proteins,NSUN6,NSUN7,and ALYREF in brain tissue are indicated in individuals with Alzheimer's disease,individuals with a high neuropathological load or have suffered traumatic brain injury.Likewise,an abundance of m^(6)A reader and anti-reader proteins are reported to change across brain regions in Lewy bodies diseases,Alzheimer's disease,and individuals with high cognitive reserve.m^(6)A-modified RNAs are also reported significantly more abundant in dementia with Lewy bodies brain tissue but significantly reduced in Parkinson's disease tissue,whilst modified RNAs are misplaced within diseased cells,particularly where synapses are located.In parahippocampal brain tissue,m^(6)A modification is enriched in transcripts associated with psychiatric disorders including conditions with clear cognitive deficits.These findings indicate a diverse set of molecular mechanisms are influenced by RNA methylation systems that can cause neuronal and synaptic dysfunction underlying neurocognitive disorders.Targeting these RNA modification systems brings new prospects for neural regenerative therapies.
基金supported by the National Natural Science Foundation of China(81970841,82101160,82121003)the Department of Science and Technology of Sichuan Province(2023ZYD0172,2023YFS0161)+3 种基金the program of Science and Technology International Cooperation Project of Qinghai province(China)(No.2022-HZ-814)Sichuan Intellectual Property Office(China)(No.2022-ZS-0070)the CAMS Innovation Fund for Medical Sciences(2019-12M-5-032)Open Project of Henan Provincial Key Laboratory of Ophthalmology and Visual Science(20KFKT02).
文摘Inherited retinal dystrophies (IRDs) are major causes of visual impairment and irreversible blindness worldwide, while the precise molecular and genetic mechanisms are still elusive. N6-methyladenosine (m^(6)A) modification is the most prevalent internal modification in eukaryotic mRNA. YTH domain containing 2 (YTHDC2), an m^(6)A reader protein, has recently been identified as a key player in germline development and human cancer. However, its contribution to retinal function remains unknown. Here, we explore the role of YTHDC2 in the visual function of retinal rod photoreceptors by generating rod-specific Ythdc2 knockout mice. Results show that Ythdc2 deficiency in rods causes diminished scotopic ERG responses and progressive retinal degeneration. Multi-omics analysis further identifies Ppef2 and Pde6b as the potential targets of YTHDC2 in the retina. Specifically, via its YTH domain, YTHDC2 recognizes and binds m^(6)A-modified Ppef2 mRNA at the coding sequence and Pde6b mRNA at the 5′-UTR, resulting in enhanced translation efficiency without affecting mRNA levels. Compromised translation efficiency of Ppef2 and Pde6b after YTHDC2 depletion ultimately leads to decreased protein levels in the retina, impaired retinal function, and progressive rod death. Collectively, our finding highlights the importance of YTHDC2 in visual function and photoreceptor survival, which provides an unreported elucidation of IRD pathogenesis via epitranscriptomics.
基金Supported by the National Natural Science Foundation of China,No.82171039.
文摘BACKGROUND Cataracts remain a prime reason for visual disturbance and blindness all over the world,despite the capacity for successful surgical replacement with artificial lenses.Diabetic cataract(DC),a metabolic complication,usually occurs at an earlier age and progresses faster than age-related cataracts.Evidence has linked N6-methyladenosine(m6A)to DC progression.However,there exists a lack of understanding regarding RNA m6A modifications and the role of m6A in DC pathogenesis.AIM To elucidate the role played by altered m6A and differentially expressed mRNAs(DEmRNAs)in DC.METHODS Anterior lens capsules were collected from the control subjects and patients with DC.M6A epitranscriptomic microarray was performed to investigate the altered m6A modifications and determine the DEmRNAs.Through Gene Ontology and pathway enrichment(Kyoto Encyclopedia of Genes and Genomes)analyses,the potential role played by dysregulated m6A modification was predicted.Real-time polymerase chain reaction was further carried out to identify the dysregulated expression of RNA methyltransferases,demethylases,and readers.RESULTS Increased m6A abundance levels were found in the total mRNA of DC samples.Bioinformatics analysis predicted that ferroptosis pathways could be associated with m6A-modified mRNAs.The levels of five methylation-related genes-RBM15,WTAP,ALKBH5,FTO,and YTHDF1-were upregulated in DC samples.Upregulation of RBM15 expression was verified in SRA01/04 cells with high-glucose medium and in samples from DC patients.CONCLUSION M6a mRNA modifications may be involved in DC progression via the ferroptosis pathway,rendering novel insights into therapeutic strategies for DC.
基金supported by the National Nature Science Foundation of China(Grant No.31660568)Guangxi Science and Technology major project(Grant No.GuikeAA22068088)+2 种基金start-up funding for introduced talents in Guangxi University,the Guangxi Colleges and Universities Young and Middle-aged Teachers'Basic Scientific Research Ability Improvement Project(Grant No.2024KY0010)Guangxi Graduate Education Innovation Program(Grant No.YCSW2024093)the Guangxi University Student Innovation and Entrepreneurship Training Program Funding Project(Grant Nos.202310593704,202310593714,202410953044S).
文摘N6-methyladenosine(m^(6)A)modification,the most abundant internal modification in messenger RNA(mRNA)and long non-coding RNA(lncRNA),has emerged as a critical epitranscriptomic regulatory mechanism in eukaryotes.While the importance of m^(6)A modification in various biological processes has been recognized,a comprehensive understanding of its diverse roles in plant biology and agricultural applications remains fragmented.This review analyzes recent advances inm^(6)A modification's biological functions in plants.m^(6)A modification plays crucial roles in multiple aspects of plant life,including seed germination,organ development,and reproductive structure formation.Furthermore,m^(6)A has been found to significantly influence plant responses to environmental stresses,including salt,drought,temperature,and heavy metal exposure.We also uncover m^(6)A involvement in important agricultural traits.This review provides insights into the mechanistic understanding of m^(6)A modification in plants and highlights its applications in agricultural improvement,offering a foundation for future research in crop enhancement and stress resistance.
基金supported by the National Key Research and Development Program of China(2021YFC2700100)the Natural Science Foundation of Zhejiang Province(LD22C060001)+2 种基金the National Natural Science Foundation of China(31930031)the fellowship of China National Postdoctoral Program for Innovative Talents(BX20230031)Beijing Natural Science Foundation(7244435).
文摘Proper ovarian follicle development,which is required for the maintenance of female fertility,is critical for the production of mature oocytes[1,2].Meanwhile,the correct establishment of the epitranscriptome in oocytes is essential for precise gene repression and the acquisition of developmental competence[1–5].The ac4C modification is the third most abundant chemical modification in transcriptome[6,7].NAT10,the only known writer of ac4C,has been shown to participate in physiological and disease settings[6,8–11].However,NAT10-targeted transcripts in oocytes as well as their functions in supporting folliculogenesis are poorly understood.
基金supported by the Mid-Career Researcher Program through the National Research Foundation of Korea funded by the Ministry of Science,ICT,and Future Planning(NRF-2021R1A2C1004187)Republic of Korea+3 种基金the Qing Lan Project of Jiangsu Province(2024)the Natural Science Foundation of Jiangsu Province(grant NoBK20241054)the Program of the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(23KJB550004)the High-Level Innovation and Entrepreneurship Talents Introduction Program of Jiangsu Province of China(JSSCBS20230419).
文摘Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in the process of plant stress adaptation.Currently,over 170 distinct chemical modifications have been identified in mRNAs,tRNAs,rRNAs,microRNAs(miRNAs),and long noncoding RNAs(lncRNAs).Genetic and molec-ular studies have identified the genes responsible for addition and removal of chemical modifications from RNA molecules,which are known as"writers"and"erasers,"respectively.N^(6)-methyladenosine(m^(6)A)is the most prevalent chemical modification identified in eukaryotic mRNAs.Recent studies have identified m6 A writers and erasers across different plant species,including Arabidopsis(Arabidopsis thaliana),rice(Oryza sativa),cotton(Gossypium hirsutum),and tomato(Solanum lycopersicum).Accumulating discoveries have improved our understanding of the functions of RNA modifications in plant stress responses.This review highlights the latest research on RNA modification,emphasizing the biological and cellular roles of diverse chemical modifications of mRNAs,tRNAs,rRNAs,miRNAs,and lncRNAs in plant responses to environ-mental and hormonal signals.We also propose and discuss critical questions and future challenges for enhancing our understanding of the cellular and mechanistic roles of RNA modifications in plant stress re-sponses.Integrating molecular insights into the regulatory roles of RNA modifications in stress responses with novel genome-and RNA-editing technologies will facilitate the breeding of stress-tolerant crops through precise engineering of RNA modifications.
基金supported by the Scientific Research and Innovation Team of the First Affiliated Hospital of Zhengzhou University(ZYCXTD202310)the Medical Science and Technology Research Project of Henan Province(SBGJ202302045)。
文摘5-methylcytosine(m^(5)C)is a prevalent RNA modification that has various impacts on m RNA fate.Here,we generated 30 single-base resolution RNA m^(5)C methylomes and revealed the dynamic nature of m^(5)C of heart,muscle,lung,esophagus,stomach,pancreas,colon,jejunum,and rectum from 7 adult human individuals using RNA-Bis Seq.Based on clustering analysis,the heart and muscle formed one cluster,while the remaining tissues constituted another cluster.Intriguingly,we observed a discrepancy pattern between m^(5)C levels and gene expression in these tissues when comparing the m^(5)C methylome and transcriptome.Moreover,we identified differences in NSUN2-mediated m^(5)C modifications between esophageal paracancerous tissues and healthy individual tissues.Notably,NSUN2 was found to interact with PLXNA1 m RNA,and silencing NSUN2 in esophageal squamous cell carcinoma(ESCC)cells resulted in the downregulation of PLXNA1 expression through an m^(5)C-mediated mechanism.Overall,our study provides valuable insights into the m^(5)C profile and the relationship between the methylome and transcriptome in human tissues,highlighting the potential role of m^(5)C modification as an epitranscriptomic biomarker.
基金supported by the National Key Research and Development Program ofChina(2019YFA0802600,2022YFC2702600)Research Funds of Center for Advanced Interdisciplinary Science and Biomedicine of IHM"(QYPY20230032)+4 种基金the National Natural Science Foundation of China(31970793,32170856 and 32300711)the Anhui Provincial Natural Science Foundation grant(2408085jJ016)the Reproductive and Genetic Hospital of CITIC-XIANGYA(YNXM-202211)the Hunan Provincial Grant for Innovative Province Construction(2019SK4012)the Hundred Youth Talents Program of Hunan Province.
文摘Male fertility is built on the proper proliferation and differentiation of germline cells within the seminiferous epithelium in the testis,which continuously produces millions of sperm per day in mammals[1].RNA modifications are emerging as crucial epitranscriptomic regulators.
基金supported by the National Natural Science Foundation of China(32372666)the Project of the National Key Laboratory of Tropical Crop Breeding(NKLTCB-RC202402 and NKLTCBCXTD26)the Central Public-interest Scientific Institution Basal Research Fund for the Chinese Academy of Tropical Agricultural Sciences(1630052024024).
文摘The emerging field of epitranscriptomics has revolutionized our understanding of post-transcriptional regulation in plant systems.This review focuses on cutting-edge discoveries in the area of RNA modification,with a particular emphasis on the N^(6)-methyladenosine(m^(6)A)-mediated regulatory networks that govern plant development and fruit maturation.We systematically summarize the spatiotemporal patterns of RNA modifications and their integration into phytohormone signaling cascades and responses to environmental stimuli.Advanced epitranscriptome sequencing platforms have identified evolutionarily conserved modification signatures across angiosperm species,while simultaneously revealing species-specific regulatory architectures.Despite substantial progress,our understanding of the molecular mechanisms that underlie RNA modifications,especially those other than m^(6)A,remains limited.We propose an innovative roadmap that combines CRISPR-based writer/eraser manipulation,single-cell spatial epitranscriptomics,and synthetic biology approaches to harness RNA modification networks for precision agriculture.We also underscore the importance of interdisciplinary collaboration that integrates findings from biology,chemistry,physics,and computer science to decode the plant epitranscriptome.To enable precise control of postharvest physiology,future priorities should include the development of biosensors for specific modification types,the engineering of RNA modification–dependent translation control systems,and the development of RNA epigenetic editing tools.
基金A.Bendahmane and A.Boualem are supported by Saclay Plant Sciences(SPS)(ANR-17-EUR-0007)the NectarGland ERC Project(101095736)+1 种基金Explor'ae ANR-24-RRll-0003the Plant Biology and Breeding Department of INRAE.
文摘For a long time,mutations that do not alter protein sequences,so-called synonymous mutations,were largely overlooked.Scientists assumed they had little to no biological impact,considering them as neutral background noise in the course of evolution.But a new study by Xin et al.(2025)challenges that assumption.Their research reveals that one such"silent"mutation played a pivotal role in cucumber domestication(Che and Zhang,2019).Rather than being inert,the mutation triggered a cascade of molecular changes involving mRNA structure and chemical modifications,ultimately altering hormone levels and growth patterns.These findings mark a turning point in our understanding of gene regulation,exposing RNA,not just DNA or protein,as a major driver of evolutionary change.
基金supported by the“Centro de Investigacion Biomédica en Red Fisiopatología de la Obesidad y Nutricion”,which is an initiative of the“Instituto de Salud Carlos III”(ISCIII)of Spain,financed by the European Regional Development Fund under“A way to make Europe"/"Investing in your future”(CB06/03),a grant from ISCIII(No.PI18/01399,PI21/00633)UMA-FEDERJA-085,from Programa Operativo FEDER 2014–2020 of the Consejería de Economía y Conocimiento de la Junta de Andalucía+4 种基金a grant from the Consejeria Universidad,Investigacion e Innovacion Junta de Andalucia(No.PY20-01270,PI0293-2019)H.B.was supported by a predoctoral fellowship“Plan Propio IBIMA 2020 A.1 Contratos predoctorales”(No.predoc20_002)by a“Sara Borrell”postdoctoral contract(No.CD22/00053)from the Instituto de Salud Carlos III—Madrid(Spain),“Financiado por la Unión Europea—NextGenerationEU”,and the plan Recuperación,Transformación y Resiliencia.L.A.G.-F.was supported by a“Sara Borrell”postdoctoral contract(No.CD21/000131)from the Instituto de Salud Carlos III—Madrid(Spain)G.M.M.-N.was supported by a postdoctoral contract from the University of Malaga(No.UMA20-FEDERJA-092)M.M.G.was the recipient of the Nicolas Monardes Programme from the“Servicio Andaluz de Salud,Junta de Andalucia”,Spain(No.RC-0001-2018,C-0029-2014).
文摘Colorectal cancer(CRC)continues to be the third most frequently diagnosed cancer,and the second leading cause of cancer-related mortality.Several non-invasive biomarkers have emerged,but only a few have been incorporated into clinical practice due to the lack of sensitivity.1 Research on the epigenome has unveiled potential clinical applications for diagnosis and therapy response.2,3 Particularly,recent evidence suggests a novel role of RNA methylation in the development of CRC,4 revealing an overall RNA m6A hypomethylation.5 However,our understanding of their contribution to CRC remains limited.
基金supported by the National Natural Science Foundation of China awarded to SL(Grant No.31500601)and CX(Grants Nos.31570737 and 31770806)supported by the“1000 Young Talents Program”of China
文摘Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N^6-methyladenosine （m^6A） is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs （lncRNAs）. In mammalian cells, m^6A can be incorporated by a methyltransferase complex and removed by demethy- lases, which ensures that the m^6A modification is reversible and dynamic. Moreover, m^6A is recognized by the YT521-B homology （YTH） domain-containing proteins, which subsequently direct different complexes to regulate RNA signaling pathways, such as RNA metabolism, RNA splicing, RNA folding, and protein translation. Herein, we summarize the recent progresses made in understanding the molecular mechanisms underlying the m^6A recognition by YTH domaincontaining proteins, which would shed new light on m^6A-specific recognition and provide clues to the future identification of reader proteins of many other RNA modifications.
基金supported by the National Basic Research Program of China (Grant Nos. 2016YFC0900302 and 2017YFA0505201)the National Natural Science Foundation of China (Grant No. 21432002)
文摘More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from Na-methyladenosine （m6A）, N1-methyladenosine （mXA） has been found as a reversible modification in tRNA and mRNA. mlA occurs at positions 9, 14, and 58 of tRNA, with m1A58 being critical for tRNA stability. Other than the hundreds of m1A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1A also identifies 〉 20 m1A sites in mitochondrial genes, m1A in the coding region of mitochondrial transcripts can inhibit the translation of the corresponding proteins. In this review, we summarize the current understanding of mlA in mRNA and tRNA, covering high-throughput sequencing methods developed for m1A methylome, m1A-related enzymes （writers and erasers）, as well as its functions in mRNA and tRNA.
基金supported by the National Natural Science Foundation of China(22225704,21820102008,92053109)the National Basic Research Program of China(2019YFA0802201)the Beijing Natural Science Foundation(Z200010).
文摘N6-Methyladenosine(m^(6)A)is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation,including transcriptional and post-transcriptional regulation.m^(6)A is a reversible modification that is installed,removed,and recognized by methyltransferases(writers),demethylases(erasers),and m^(6)A-binding proteins(readers),respectively.Recently,the breadth of research on m^(6)A in plants has expanded,and the vital roles of m^(6)A in plant development,biotic and abiotic stress responses,and crop trait improvement have been investigated.In this review,we discuss recent developments in research on m^(6)A and highlight the detection methods,distribution,regulatory proteins,and molecular and biological functions of m^(6)A in plants.We also offer some perspectives on future investigations,providing direction for subsequent research on m^(6)A in plants.
基金supported by the National Key R&D Program of China(2019YFA0802202)the National Natural Science Foundation of China(91940304,31971228,31900903,31970604,32100467,32225011)the Youth Science and Technology Innovation Talent of Guangdong Te Zhi Plan(2019TQ05Y181)。
文摘2′-O-methylation(Nm)is one of the most abundant RNA epigenetic modifications and plays a vital role in the post-transcriptional regulation of gene expression.Current Nm mapping approaches are normally limited to highly abundant RNAs and have significant technical hurdles in m RNAs or relatively rare non-coding RNAs(nc RNAs).Here,we developed a new method for enriching Nm sites by using RNA exoribonuclease and periodate oxidation reactivity to eliminate 2′-hydroxylated(2′-OH)nucleosides,coupled with sequencing(Nm-REP-seq).We revealed several novel classes of Nm-containing nc RNAs as well as m RNAs in humans,mice,and drosophila.We found that some novel Nm sites are present at fixed positions in different t RNAs and are potential substrates of fibrillarin(FBL)methyltransferase mediated by sno RNAs.Importantly,we discovered,for the first time,that Nm located at the 3′-end of various types of nc RNAs and fragments derived from them.Our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.
基金support from the National Natural Science Foundation of China(32070613,32270623)the Science and Technology Innovation Program of Hunan Province(2021RC3045)+1 种基金support from the National Natural Science Foundation of China(U20A2029)support from the Postgraduate Scientific Research Innovation Project of Hunan Province(CX20200468).
文摘Acetylation of N^(4)-cytidine(ac^(4)C)has recently been discovered as a novel modification of mRNA.RNA ac^(4)C modification has been shown to be a key regulator of RNA stability,RNA translation,and the thermal stress response.However,its existence in eukaryotic mRNAs is still controversial.In plants,the existence,distribution pattern,and potential function of RNA ac^(4)C modification are largely unknown.Here we report the presence of ac^(4)C in the mRNAs of both Arabidopsis thaliana and rice(Oryza sativa).By comparing two ac^(4)C sequencing methods,we found that RNA immunoprecipitation and sequencing(acRIP-seq),but not ac^(4)C sequencing,was suitable for plant RNA ac^(4)C sequencing.We present transcriptome-wide atlases of RNA ac^(4)C modification in A.thaliana and rice mRNAs obtained by acRIP-seq.Analysis of the distribution of RNA ac^(4)C modifications showed that ac^(4)C is enriched near translation start sites in rice mRNAs and near translation start sites and translation end sites in Arabidopsis mRNAs.The RNA ac^(4)C modification level is positively correlated with RNA half-life and the number of splicing variants.Similar to that in mammals,the translation efficiency of ac^(4)C target genes is significantly higher than that of other genes.Our in vitro translation results confirmed that RNA ac^(4)C modification enhances translation efficiency.We also found that RNA ac^(4)C modification is negatively correlated with RNA structure.These results suggest that ac^(4)C is a conserved mRNA modification in plants that contributes to RNA stability,splicing,translation,and secondary structure formation.
基金supported by the Earmarked Fund for China Agriculture Research System of Ministry of Finance and Ministry of Agriculture and Rural Affairs(Grant No.CARS-19)the Scientific Research Foundation of Graduate School of Fujian Agriculture and Forestry University(Grant No.324-1122yb070)+7 种基金the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University(Grant No.2019B01)the Rural Revitalization Tea Industry Technical Service Project of Fujian Agriculture and Forestry University(Grant No.11899170145)the“Double first-class”scientific and technological innovation capacity and enhancement cultivation plan of Fujian Agriculture and Forestry University(Grant No.KSYLP004)the 6.18 Tea Industry Technology Branch of Collaborative Innovation Institute(Grant No.K1520001A)the Fujian Agriculture and Forestry University Construction Project for Technological Innovation and Service System of Tea Industry Chain(Grant No.K1520005A01)the Construction of Plateau Discipline of Fujian Province(Grant No.102/71201801101)the Tea Industry Branch of Collaborative Innovation Institute of Fujian Agriculture and Forestry University(Grant No.K1521015A)the Special Fund for Science and Technology Innovation of Fujian Zhang Tianfu Tea Development Foundation(Grant No.FJZTF01),China.
文摘The epitranscriptomic mark N6-methyladenosine(m^(6)A),which is the predominant internal modification in RNA,is important for plant responses to diverse stresses.Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor.However,the effects of the m^(6)A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized.We performed an integrated RNA methylome and transcriptome analysis to explore the m^(6)Amediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea(Camellia sinensis)leaves under solar-withering conditions.Dynamic changes in global m^(6)A level in tea leaves were mainly controlled by two m^(6)A erasers(CsALKBH4A and CsALKBH4B)during solar-withering treatments.Differentially methylated peak-associated genes following solarwithering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways.Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid,catechin,and theaflavin contents by triggering alternative splicing-mediated regulation.Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m^(6)A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.
